5I5S

X-RAY CRYSTAL STRUCTURE AT 2.06A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BENZISOXAZOLE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn-house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293MDL MORPHEUS SCREEN CONDITION B2, DTT.
Crystal Properties
Matthews coefficientSolvent content
2.3547.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.852α = 90
b = 105.985β = 90
c = 107.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A200VARIMAX HF2010-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.06107.2799.718.85.249096
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.171000.4830.4830.5920.2531.65.27092

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTIn-house structure2.062046455247399.320.17390.17110.2264RANDOM34.401
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.910.741.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.387
r_dihedral_angle_4_deg14.228
r_dihedral_angle_3_deg11.914
r_dihedral_angle_1_deg4.355
r_mcangle_it3.965
r_mcbond_it2.63
r_mcbond_other2.626
r_angle_refined_deg1.43
r_angle_other_deg0.739
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.387
r_dihedral_angle_4_deg14.228
r_dihedral_angle_3_deg11.914
r_dihedral_angle_1_deg4.355
r_mcangle_it3.965
r_mcbond_it2.63
r_mcbond_other2.626
r_angle_refined_deg1.43
r_angle_other_deg0.739
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5733
Nucleic Acid Atoms
Solvent Atoms688
Heterogen Atoms110

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing